WHIRLY1 overexpression in barley delayed drought-induced leaf senescence and suppressed drought-induced increases in ABA concentration and ABA-dependent marker genes HvNCED1 and HvS40. RNAseq revealed that WHIRLY1 overexpression prevented drought-induced upregulation of stress- and ABA-related genes but promoted genes related to primary metabolism and growth, indicating WHIRLY1 balances stress response and developmental pathways. Crucially, WHIRLY1 overexpression decreased levels of euchromatic marks H3K4me3 and H3K9ac at the HvNCED1 and HvS40 promoters and transcriptional start sites. This demonstrates that WHIRLY1, acting as a retrograde signal, modulates ABA-related nuclear gene expression reprogramming during drought via differential histone modifications.

Analysis identified 117 barley genes involved in DNA methylation, histone modification, and chromatin remodeling. RNAseq revealed distinct gene expression profiles during dark-induced leaf senescence (DILS) compared to developmental leaf senescence (DLS) and controls. Western blot showed increased H3K4me3 and H3K9me2 methylation during both DILS and DLS. H3K9ac acetylation decreased significantly during DILS but remained unchanged during DLS. These findings indicate different epigenetic regulation of senescence types and suggest an epigenetically regulated molecular switch between cell survival and death in DILS.

ChIP-seq mapping of nine histone modifications in barley seedlings defined four modification classes and ten chromatin states. Five states map to genes and five to intergenic regions. H3K36me3-associated genic states correlate with constitutive expression, while an H3K27me3-containing genic state associates with differential expression. Chromosomes comprise three global environments: telomere-proximal regions feature high H3K27me3 density covering genes and intergenic DNA with low H3K27me1; gene-rich interior regions show active chromatin states, decreased H3K27me3, and increased H3K27me1/H3K9me2; pericentromeric regions contain H3K27me3-depleted retrotransposon-rich areas marked by abundant H3K27me1 and H3K9me2. Intergenic H3K27me3 specifies facultative heterochromatin in telomere-proximal regions, while H3K27me1 marks constitutive heterochromatin elsewhere.

Both maleic acid hydrazide (MH) and gamma ray mutagens significantly alter global histone methylation and acetylation levels in barley. Gamma irradiation exerts a stronger effect on DNA methylation levels compared to MH. This study provides the first immunohistochemical evidence linking mutagenic treatments to specific epigenetic modifications.

The awn is a bristle-like extension from the tip of the lemma in grasses. In barley, the predominant cultivars possess long awns that contribute to grain yield and quality through photosynthesis. In addition, various awn morphological mutants are available in barley, rendering it a useful cereal crop to investigate the mechanims of awn development. Here, we identified the gene causative of the short and crooked awn (sca) mutant, which exhibits a short and curved awn phenotype. Intercrossing experiments revealed that the sca mutant induced in the Japanese cultivar (cv.) "Akashinriki" is allelic to the independently isolated moderately short-awn mutant breviaristatum-a (ari-a). Map-based cloning and sequencing revealed that SCA encodes the Polycomb group-associated protein EMBRYONIC FLOWER 1. We found that SCA affects awn development through the promotion of cell proliferation, elongation, and cell wall synthesis. RNA sequencing of cv. Bowman backcross-derived near-isogenic lines of sca and ari-a6 alleles showed that SCA is directly or indirectly involved in promoting the expression of genes related to awn development. Additionally, SCA represses various transcription factors essential for floral organ development and plant architecture, such as MADS-box and Knotted1-like homeobox genes. Notably, the repression of the C-class MADS-box gene HvMADS58 by SCA in awns is associated with the accumulation of the repressive histone modification H3K27me3. These findings highlight the potential role of SCA-mediated gene regulation, including histone modification, as a novel pathway in barley awn development.

Genetic mapping places markers differently than physical mapping in barley chromosome 3H's recombination-poor centromere. FISH with 70 single-copy probes from 65 genetically assigned BAC contigs revealed the centromeric 5.5 cM bin spans 58% of the mitotic metaphase chromosome length. Mitotic and meiotic chromatin in this recombination-poor region is enriched for the heterochromatic mark H3K9me2. In contrast, recombination-enriched subterminal regions are enriched in euchromatic marks H3K4me2, H3K4me3, and H3K27me3. This suggests the meiotic recombination rate is influenced by the chromatin landscape.

Vernalization in barley promotes flowering by epigenetically activating HvVRN1. Pre-vernalization repression associates with high H3K27me3 at HvVRN1 chromatin. Vernalization increases H3K4me3 and decreases H3K27me3, establishing an active chromatin state. This state maintenance constitutes the epigenetic memory of vernalization in cereals. Unlike Arabidopsis, where vernalization epigenetically represses the floral repressor FLC, cereals epigenetically activate the floral promoter VRN1.

Four barley Polycomb group (PcG) homologues, HvFIE, HvE(Z), HvSu(z)12a, and HvSu(z)12b, exhibit differential expression across tissues and seed developmental stages and between cultivars with different seed sizes. HvFIE and HvE(Z) expression is responsive to abscisic acid (ABA), implying association with ABA-mediated epigenetic processes during seed development, germination, and stress response. These PcG genes may regulate barley seed development.